Package evaluation to test SnpArrays on Julia 1.14.0-DEV.3141 (fbd24f51d0*) started at 2026-09-09T00:43:34.662 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.18s ################################################################################ # Installation # Installing SnpArrays... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [4e780e97] + SnpArrays v0.3.23 Updating `~/.julia/environments/v1.14/Manifest.toml` [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.30.1 [67c07d97] + Automa v1.2.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.17 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.9 [6b39b394] + CodecZstd v0.8.7 [f70d9fcc] + CommonWorldInvalidations v1.2.2 [34da2185] + Compat v4.18.1 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.6 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [615f187c] + IfElse v0.1.1 ⌅ [842dd82b] + InlineStrings v1.4.6 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [b964fa9f] + LaTeXStrings v1.4.1 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v1.0.1 [bdcacae8] + LoopVectorization v0.12.174 [d125e4d3] + ManualMemory v0.1.8 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v2.0.1 ⌅ [69de0a69] + Parsers v2.8.8 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.4.8 [43287f4e] + PtrArrays v1.4.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.46 [431bcebd] + SciMLPublic v1.3.0 [91c51154] + SentinelArrays v1.4.10 [4e780e97] + SnpArrays v0.3.23 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.9.0 [aedffcd0] + Static v1.4.6 [0d7ed370] + StaticArrayInterface v1.10.0 [10745b16] + Statistics v1.11.5 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.13 ⌅ [892a3eda] + StringManipulation v0.5.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.14.0 [8290d209] + ThreadingUtilities v0.5.6 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.74 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [ffd25f8a] + XZ_jll v5.8.3+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0 [4536629a] + OpenBLAS_jll v0.3.34+0 [05823500] + OpenLibm_jll v0.8.8+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.67s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 3.9 s ✓ CodecZstd 18.5 s ✓ Automa 1.8 s ✓ CodecBzip2 26.9 s ✓ CSV [ Info: Compiling VCF parser... 15.6 s ✓ VariantCallFormat 24.6 s ✓ SnpArrays 6 dependencies successfully precompiled in 92 seconds. 181 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 118.69s ################################################################################ # Testing # Testing SnpArrays Status `/tmp/jl_QO96Gx/Project.toml` [79e6a3ab] Adapt v4.7.0 [336ed68f] CSV v0.10.17 [052768ef] CUDA v6.3.1 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.9 [6b39b394] CodecZstd v0.8.7 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [c27321d9] Glob v1.5.0 [bdcacae8] LoopVectorization v0.12.174 [e1d29d7a] Missings v1.2.0 [ae029012] Requires v1.3.1 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.9.0 [10745b16] Statistics v1.11.5 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v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.9 [6b39b394] CodecZstd v0.8.7 [f70d9fcc] CommonWorldInvalidations v1.2.2 [34da2185] Compat v4.18.1 [9db33cc3] CompilerCaching v0.5.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.2.0 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.6 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [ffbed154] DocStringExtensions v0.9.5 [e2ba6199] ExprTools v0.1.11 [48062228] FilePathsBase v0.9.24 [0c68f7d7] GPUArrays v11.5.14 [46192b85] GPUArraysCore v0.2.0 [61eb1bfa] GPUCompiler v2.5.4 [096a3bc2] GPUToolbox v3.0.0 [c27321d9] Glob v1.5.0 [076d061b] HashArrayMappedTries v0.2.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [615f187c] IfElse v0.1.1 ⌅ [842dd82b] InlineStrings v1.4.6 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [63c18a36] KernelAbstractions v0.9.42 [929cbde3] LLVM v9.13.1 [8b046642] LLVMLoopInfo v1.0.0 [11f193de] LMDB v3.0.1 [b964fa9f] LaTeXStrings v1.4.1 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v1.0.1 [bdcacae8] LoopVectorization v0.12.174 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [e1d29d7a] Missings v1.2.0 [611af6d1] NVML v6.3.1 [5da4648a] NVTX v1.0.3 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v2.0.1 ⌅ [69de0a69] Parsers v2.8.8 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.4.8 [43287f4e] PtrArrays v1.4.0 [74087812] Random123 v1.7.1 [e6cf234a] RandomNumbers v1.6.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.46 [431bcebd] SciMLPublic v1.3.0 [7e506255] ScopedValues v1.6.2 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.10 [4e780e97] SnpArrays v0.3.23 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.9.0 [aedffcd0] Static v1.4.6 [0d7ed370] StaticArrayInterface v1.10.0 [90137ffa] StaticArrays v1.9.20 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.5 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.13 ⌅ [892a3eda] StringManipulation v0.5.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.14.0 [8290d209] ThreadingUtilities v0.5.6 [e689c965] Tracy v0.1.6 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [3a884ed6] UnPack v1.0.2 [013be700] UnsafeAtomics v0.3.2 [28eba6e3] VariantCallFormat v0.5.9 [3d5dd08c] VectorizationBase v0.21.74 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [182d3088] cuBLAS v6.3.1 [533571aa] cuFFT v6.3.1 [20fd9a0b] cuRAND v6.3.1 [887afef0] cuSOLVER v6.3.1 [b26da814] cuSPARSE v6.3.1 [6e34b625] Bzip2_jll v1.0.9+0 [d1e2174e] CUDA_Compiler_jll v0.6.2+0 [4ee394cb] CUDA_Driver_jll v13.3.4+0 [76a88914] CUDA_Runtime_jll v0.24.4+2 [9c1d0b0a] JuliaNVTXCallbacks_jll v0.2.1+0 [dad2f222] LLVMExtra_jll v0.0.47+0 [6206cf0b] LMDB_jll v1.0.0+0 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[ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.5.7+0 [deac9b47] LibCURL_jll v8.22.0+0 [e37daf67] LibGit2_jll v1.9.7+0 [29816b5a] LibSSH2_jll v1.11.104+0 [14a3606d] MozillaCACerts_jll v2026.8.13 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.8+0 [458c3c95] OpenSSL_jll v3.5.8+0 [efcefdf7] PCRE2_jll v10.48.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time size | 8 8 2.6s Test Summary: | Pass Total Time counts | 10 10 2.2s Test Summary: | Pass Total Time means | 33 33 1.7s Test Summary: | Pass Total Time var/std | 10 10 1.9s Test Summary: | Pass Total Time missingpos | 3 3 2.3s Test Summary: | Pass Total Time create bed | 4 4 1.8s Test Summary: | Pass Total Time convert | 12 12 2.7s Test Summary: | Pass Total Time convert (ADMIXTURE) | 3 3 0.0s Test Summary: | Pass Total Time maf | 4 4 2.1s convert genotype: 0.73 seconds Φ = GG': 0.37 seconds convert G to {0,1} matrix: 0.02 seconds S = GG': 0.36 seconds Test Summary: | Pass Total Time grm | 11 11 13.5s Test Summary: | Pass Total Time filter | 8 8 10.8s ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time SnpBitMatrix-vector multiplication | 48 48 43.3s ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time copyto bitmatrix | 36 36 14.8s ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time convert (SnpBitMatrix) | 24 24 11.1s Test Summary: | Pass Total Time copyto SnpLinAlg | 36 36 8.8s Test Summary: | Pass Total Time convert (SnpLinAlg) | 24 24 8.5s Test Summary: | Pass Total Time SnpLinAlg-vector multiplication (zeroimpute) | 48 48 1m48.9s Test Summary: | Pass Total Time SnpLinAlg-matrix multiplication zeroimpute | 48 48 50.1s Test Summary: | Pass Total Time SnpLinAlg-vector multiplication (Miter > 0) | 1 1 12.5s Test Summary: | Pass Total Time SnpLinAlg-vector multiplication meanimpute | 48 48 1m05.2s Test Summary: | Pass Total Time SnpLinAlg-matrix multiplication meanimpute | 48 48 38.0s ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time subarrays | 4 4 7.6s 0.418850 seconds (244.21 k allocations: 14.803 MiB, 94.19% compilation time) 5.314516 seconds (985.61 k allocations: 62.136 MiB, 99.85% compilation time) 0.139517 seconds (51.34 k allocations: 3.263 MiB, 99.82% compilation time) 0.142726 seconds (40.96 k allocations: 3.219 MiB, 99.76% compilation time) 12.131398 seconds (6.23 M allocations: 377.948 MiB, 2.50% gc time, 99.48% compilation time) Test Summary: | Pass Total Time split-merge-readwrite | 20 20 1m06.7s 0.168689 seconds 0.176259 seconds 0.133934 seconds 0.139979 seconds 0.131980 seconds 0.139600 seconds 0.157728 seconds 0.138914 seconds 0.196133 seconds 0.150907 seconds 0.136876 seconds 0.139911 seconds Test Summary: | Pass Total Time (de)compress | 61 61 13.3s Test Summary: | Pass Total Time indexin | 3 3 2.3s Test Summary: | Pass Total Time concat | 9 9 12.7s reorder: Error During Test at /home/pkgeval/.julia/packages/SnpArrays/UNmxR/test/runtests.jl:707 Got exception outside of a @test SystemError: opening file "mouse_testreorder.bed": Permission denied Stacktrace: [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) @ Base error.jl:188 [2] open(fname::String; lock::Bool, read::Bool, write::Bool, create::Nothing, truncate::Nothing, append::Nothing) @ Base iostream.jl:332 [3] open(fname::String, mode::String; lock::Bool) @ Base iostream.jl:395 [4] open(fname::String, mode::String) @ Base iostream.jl:394 [inlined] [5] makestream(filepath::String, args::String; kwargs::@Kwargs{}) @ SnpArrays ~/.julia/packages/SnpArrays/UNmxR/src/codec.jl:9 [6] makestream(filepath::String, args::String) @ SnpArrays ~/.julia/packages/SnpArrays/UNmxR/src/codec.jl:8 [7] makestream(::SnpArrays.var"#8#9"{String}, ::String, ::Vararg{String}) @ SnpArrays ~/.julia/packages/SnpArrays/UNmxR/src/codec.jl:29 [8] SnpArray(bednm::String, m::Int64, args::String; kwargs::@Kwargs{}) @ SnpArrays ~/.julia/packages/SnpArrays/UNmxR/src/snparray.jl:35 [9] SnpArray(bednm::String, m::Int64, args::String) @ SnpArrays ~/.julia/packages/SnpArrays/UNmxR/src/snparray.jl:33 [inlined] [10] SnpArray(bednm::String, args::String; famnm::String, kwargs::@Kwargs{}) @ SnpArrays ~/.julia/packages/SnpArrays/UNmxR/src/snparray.jl:67 [11] SnpData(plink_file::String, args::String; famnm::String, bimnm::String, kwargs::@Kwargs{}) @ SnpArrays ~/.julia/packages/SnpArrays/UNmxR/src/snpdata.jl:39 [12] SnpData(plink_file::String, args::String) @ SnpArrays ~/.julia/packages/SnpArrays/UNmxR/src/snpdata.jl:21 [13] top-level scope @ ~/.julia/packages/SnpArrays/UNmxR/test/runtests.jl:708 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2252 [inlined] [15] macro expansion @ ~/.julia/packages/SnpArrays/UNmxR/test/runtests.jl:714 [inlined] Test Summary: | Error Total Time reorder | 1 1 3.0s RNG of the outermost testset: Random.Xoshiro(0xf5c12f8119be4a0c, 0x225c724ac39d3268, 0x51afab5a5713a53a, 0xf8c163cf06d73b20, 0xc28e99ce47dab946) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/SnpArrays/UNmxR/test/runtests.jl:707 Testing failed after 560.02s ERROR: LoadError: Package SnpArrays errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3298 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 738.22s: package tests unexpectedly errored